Reduced alphabets for proteins

This tool was originally created to reduce protein sequences by grouping the aminoacids in classes. During its development code to retrieve sequences with colours was added. Additionally, each aminoacid may be displayed with a distinct colour (without applying reductions).

The reduced aminoacid alphabets has been obtained from the references bellow :

Li T, Fan K, Wang J, Wang W. Reduction of protein sequence
complexity by residue grouping. Protein Eng 2003; 5:323-330.
PubMed

Murphy LR, Wallqvist A, Levy RM. Simplified amino acid alphabets
for protein fold recognition and implications for folding.
Protein Eng 2000; 13:149-152.
PubMed

Pommié C, Levadoux S, Sabatier R, Lefranc G & Lefranc MP.
IMGT standardized criteria for statistical analysis of immunoglobulin
V-REGION amino acid properties. Journal of Molecular Recognition 2004; 17:17-32.
PubMed

Spitzer M, Fuellen G, Cullen P, Lorkowski S.
VisCoSe: visualization and comparison of consensus sequences.
Bioinformatics 2004; 20:433-435.
PubMed

Wang J, Wang W. A computational approach to simplifying the protein
folding alphabet. Nat Struct Biol 1999; 11:1033-1038.
PubMed

How to define a custom reduced alphabet

The procedure is very simple:

• one letter must be used for each group of aminoacids
  p.e.: letters A,R,C,T and D for 5 groups
• aminoacid in the serie "ARNDCEQGHILKMFPSTWYV" will be substitute by letters defining the group.
  p.e: from ARNDCEQGHILKMFPSTWYV to TCDCTCDTRAACDRDTDRRA
• the resulting serie of letters will be used in the form.

Colors will be automatically assigned to each letter of the alphabet (this behavior can not be personalized at the moment)